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- PDB-2rhf: D. radiodurans RecQ HRDC domain 3 -

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Basic information

Entry
Database: PDB / ID: 2rhf
TitleD. radiodurans RecQ HRDC domain 3
ComponentsDNA helicase RecQ
KeywordsHYDROLASE / HRDC / RecQ / helicase / D. radiodurans / ATP-binding / Nucleotide-binding
Function / homology
Function and homology information


bacterial nucleoid / four-way junction helicase activity / replisome / SOS response / 3'-5' DNA helicase activity / DNA duplex unwinding / chromosome / DNA helicase / DNA recombination / DNA replication ...bacterial nucleoid / four-way junction helicase activity / replisome / SOS response / 3'-5' DNA helicase activity / DNA duplex unwinding / chromosome / DNA helicase / DNA recombination / DNA replication / hydrolase activity / DNA repair / DNA binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
DNA helicase, ATP-dependent, RecQ type, bacterial / HRDC domain / RQC domain / RQC / RQC domain / ATP-dependent DNA helicase RecQ, zinc-binding domain / RecQ zinc-binding / DNA helicase, ATP-dependent, RecQ type / Helicase and RNase D C-terminal / HRDC domain ...DNA helicase, ATP-dependent, RecQ type, bacterial / HRDC domain / RQC domain / RQC / RQC domain / ATP-dependent DNA helicase RecQ, zinc-binding domain / RecQ zinc-binding / DNA helicase, ATP-dependent, RecQ type / Helicase and RNase D C-terminal / HRDC domain / HRDC domain / HRDC domain profile. / HRDC domain superfamily / HRDC-like superfamily / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain / DNA polymerase; domain 1 / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / DNA helicase
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.1 Å
AuthorsKeck, J.L. / Killoran, M.P.
CitationJournal: Nucleic Acids Res. / Year: 2008
Title: Structure and function of the regulatory C-terminal HRDC domain from Deinococcus radiodurans RecQ.
Authors: Killoran, M.P. / Keck, J.L.
History
DepositionOct 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA helicase RecQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,5812
Polymers8,4861
Non-polymers951
Water3,081171
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.978, 49.978, 83.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-946-

HOH

DetailsAthours state that the biological molecule is unknown.

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Components

#1: Protein DNA helicase RecQ


Mass: 8486.380 Da / Num. of mol.: 1 / Fragment: D. radiodurans HRDC domain 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Strain: R1 / Gene: recQ / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q9RUU2
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.08 Å3/Da / Density % sol: 60.01 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 1.8 M Na-K Phosphate pH 4.0, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 273K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.9999, 0.9797
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 26, 2005
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.99991
20.97971
ReflectionResolution: 1.1→83.6 Å / Num. all: 42318 / Num. obs: 40879 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.067
Reflection shellResolution: 1.1→1.16 Å / Mean I/σ(I) obs: 1.8 / Rsym value: 0.419 / % possible all: 78.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
DMphasing
RefinementMethod to determine structure: MAD / Resolution: 1.1→20 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.949 / SU B: 0.76 / SU ML: 0.017 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.031 / ESU R Free: 0.031 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19399 2061 5 %RANDOM
Rwork0.17715 ---
obs0.17798 38922 96.93 %-
all-42294 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.709 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å20 Å2
2--0.28 Å20 Å2
3----0.56 Å2
Refinement stepCycle: LAST / Resolution: 1.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms588 0 5 171 764
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.022605
X-RAY DIFFRACTIONr_angle_refined_deg1.2261.988818
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.427575
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.87323.33330
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.73215106
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.587157
X-RAY DIFFRACTIONr_chiral_restr0.0950.295
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02453
X-RAY DIFFRACTIONr_nbd_refined0.2260.2323
X-RAY DIFFRACTIONr_nbtor_refined0.3060.2431
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1110.2112
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3880.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0890.235
X-RAY DIFFRACTIONr_mcbond_it1.2531.5387
X-RAY DIFFRACTIONr_mcangle_it1.7742600
X-RAY DIFFRACTIONr_scbond_it2.4443236
X-RAY DIFFRACTIONr_scangle_it3.4064.5218
X-RAY DIFFRACTIONr_rigid_bond_restr1.423623
X-RAY DIFFRACTIONr_sphericity_free3.6193171
X-RAY DIFFRACTIONr_sphericity_bonded3.8013599
LS refinement shellResolution: 1.1→1.128 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.441 66 -
Rwork0.319 1638 -
obs--75.63 %

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